Available tools and plugins:

We are (slowly) transitioning our tools and plugins to the lab Github.
Please follow the links below for most up to date versions of each of the tools.
Where relevant please cite originating papers
For bugs/issues and queries please contact the lab here

HIT-MAP
Automated annotation and visualisation of high-resolution
spatial proteomic mass spectrometry imaging data
Platform: R (Windows, MacOS and Linux)
Now available on Github
Also available as a Docker Image here
Citation:
Guo G*, Papanicolaou M* et al. Nature Communications (2021)

Platform: Standalone Windows and MacOS application
http://galene.flimfit.org/
Citation:
Warren SC et al. eLife (2018) PubMed
Automated ECM fibre orientation and alignment script
Platform: FIJI / ImageJ
Now available on Github
Citation:
Mayorca-Guiliani AE*, Madsen CD*, Cox TR* et al. Nature Medicine (2017) PubMed
Automated Picrosirius Red (PR) analysis of collagen I using transmitted light
Platform: FIJI / ImageJ
Download v1.11
Citation:
Vennin C et al. Nature Communications (2019) PubMed
Automated Picrosirius Red (PR) birefringence (BRF) analysis of collagen I using polarised light
Platform: FIJI / ImageJ
Now available on Github
Citation:
Vennin C et al. Nature Communications (2019) PubMed
Automated Masson’s Trichrome Analysis of collagen I/bone (blue)
Platform: FIJI / ImageJ
Download v1.03
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